📦 vcftools

F

• fill-aa(1)fill in ancestral alleles✨
• fill-an-ac(1)fill or recalculate AN and AC INFO fields.✨
• fill-fs(1)Annotate VCF with flanking sequence✨
• fill-ref-md5(1)computes MD5 sum of the reference sequence✨
• fill-rsIDs(1)fill missing rsIDs✨

V

• vcf-annotate(1)annotate VCF file, add filters or custom annotations✨
• vcf-compare(1)compare bgzipped and tabix indexed VCF files✨
• vcf-concat(1)concatenate VCF files✨
• vcf-consensus(1)vcf-consensus✨
• vcf-contrast(1)finds differences amongst samples✨
• vcf-convert(1)convert between VCF versions✨
• vcf-fix-newlines(1)fix newlines in VCF file✨
• vcf-fix-ploidy(1)vcf-fix-ploidy✨
• vcf-indel-stats(1)vcf-indel-stat✨
• vcf-isec(1)create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files✨
• vcf-merge(1)merge the bgzipped and tabix indexed VCF files✨
• vcf-phased-join(1)take multiple overlapping pre-phased chunks and concatenates them into one VCF✨
• vcf-query(1)query VCF files✨
• vcf-shuffle-cols(1)reorder columns✨
• vcf-sort(1)sort VCF file✨
• vcf-stats(1)statistic of VCF file✨
• vcf-subset(1)create subset of VCF file✨
• vcf-to-tab(1)convert to tabix✨
• vcf-tstv(1)vcf-tstv✨
• vcf-validator(1)validate VCF file✨
• vcftools(1)Utilities for the variant call format (VCF) and binary variant call format (BCF)✨